Variant 7-44220272-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001220.5(CAMK2B):c.1791G>A(p.Pro597=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 1,612,312 control chromosomes in the GnomAD database, including 138,916 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10740 hom., cov: 33)

Exomes 𝑓: 0.42 ( 128176 hom. )

Consequence

CAMK2B
NM_001220.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -3.83

Variant links:

Genes affected

CAMK2B (HGNC:1461): (calcium/calmodulin dependent protein kinase II beta) The product of this gene belongs to the serine/threonine protein kinase family and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. Calcium signaling is crucial for several aspects of plasticity at glutamatergic synapses. In mammalian cells, the enzyme is composed of four different chains: alpha, beta, gamma, and delta. The product of this gene is a beta chain. It is possible that distinct isoforms of this chain have different cellular localizations and interact differently with calmodulin. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

CAMK2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 7-44220272-C-T is Benign according to our data. Variant chr7-44220272-C-T is described in ClinVar as [Benign]. Clinvar id is 1192567.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.83 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK2B	NM_001220.5 linkuse as main transcript	c.1791G>A	p.Pro597=	synonymous_variant	23/24	ENST00000395749.7	NP_001211.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK2B	ENST00000395749.7 linkuse as main transcript	c.1791G>A	p.Pro597=	synonymous_variant	23/24	1	NM_001220.5	ENSP00000379098		Q13554-1

Frequencies

GnomAD3 genomes

AF:

0.364

AC:

55317

AN:

151942

Hom.:

10736

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.448

Gnomad EAS

AF:

0.375

Gnomad SAS

AF:

0.431

Gnomad FIN

AF:

0.514

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.423

Gnomad OTH

AF:

0.343

GnomAD3 exomes

AF:

0.406

AC:

100979

AN:

248552

Hom.:

21335

AF XY:

0.411

AC XY:

55409

AN XY:

134856

show subpopulations

Gnomad AFR exome

AF:

0.208

Gnomad AMR exome

AF:

0.374

Gnomad ASJ exome

AF:

0.452

Gnomad EAS exome

AF:

0.358

Gnomad SAS exome

AF:

0.427

Gnomad FIN exome

AF:

0.511

Gnomad NFE exome

AF:

0.423

Gnomad OTH exome

AF:

0.402

GnomAD4 exome

AF:

0.415

AC:

606688

AN:

1460254

Hom.:

128176

Cov.:

AF XY:

0.416

AC XY:

301957

AN XY:

726418

show subpopulations

Gnomad4 AFR exome

AF:

0.207

Gnomad4 AMR exome

AF:

0.369

Gnomad4 ASJ exome

AF:

0.457

Gnomad4 EAS exome

AF:

0.333

Gnomad4 SAS exome

AF:

0.430

Gnomad4 FIN exome

AF:

0.508

Gnomad4 NFE exome

AF:

0.421

Gnomad4 OTH exome

AF:

0.405

GnomAD4 genome

AF:

0.364

AC:

55332

AN:

152058

Hom.:

10740

Cov.:

AF XY:

0.371

AC XY:

27563

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.219

Gnomad4 AMR

AF:

0.358

Gnomad4 ASJ

AF:

0.448

Gnomad4 EAS

AF:

0.375

Gnomad4 SAS

AF:

0.431

Gnomad4 FIN

AF:

0.514

Gnomad4 NFE

AF:

0.423

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.399

Hom.:

17968

Bravo

AF:

0.347

EpiCase

AF:

0.400

EpiControl

AF:

0.404

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

CAMK2B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 16, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Intellectual disability, autosomal dominant 54

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.94

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over